I have both Steam and a virus scanner active, and I don't recall Steam doing any searching for installed software the last time I installed it. You would lose that bet.
Sounds like a broken installation. Something got messed up somewhere, whether it was a PEBKAC error or otherwise. A clean reinstall would probably have been your best bet there. It's nothing inherent to Steam or HL2 in general, since I can tell you I installed HL2 from a physical copy of The Orange Box without any issues.
They've pretty clearly been fixing the game, not refusing to do so. As for the profile updates, I still don't know what you're talking about because you're being too vague and paranoid, but it wouldn't surprise me if there were some feature or other they added (to everyone; they aren't personally tampering with your dormant account) and they sent out an email to people that were likely to have missed it (which isn't exactly uncommon practice for customer retention). Not exactly something to be scared of.
You don't recall is not proof it doesn't happen. I say nearby during the install. I saw it. The damn thing took 3 hours from disc to main menu. Such time includes whatever it was DL'ing.
Now we're getting somewhere. Steam was broken. HL2 looked normal before one of the several times it was blocked. A forced update then broke the game. Why did I need this update? Because level 2 of the virus was installed.
It's not on purpose. The message was sent a while ago. It wasn't 'please update'. Instead they sent 'we've started tampering'. Wanna say it was a phone number or something was changed. Malware does like to collect data you know.